Detection of DNA hybridization by field-effect DNA-based biosensors: mechanisms of signal generation and open questions

First principles studies on the adsorption of rare base-pairs on the surface of B/N atom doped γ-graphyne

Rare base-pairs consists of guanine (G) paired with rare bases, such as 5-methylcytosine (5-meCyt), 5-hydroxymethylcytosine (5-hmCyt), 5-carboxylcytosine (5-caCyt), and 5-formylcytosine (5-fCyt), have become the focus of epigenetic research because they can be used as markers to detect some chronic diseases and cancers. However, the correlation detection of these rare base-pairs is limited, which in turn limits the development of diagnostic tests and devices. Herein, the interaction of rare base-pairs adsorbed on pure and B/N-doped γ-graphyne (γ-GY) nanosheets was explored using the density functional theory. The calculated adsorption energy showed that the system of rare base-pairs on B-doped γ-GY is more stable than that on pure γ-GY or N-doped γ-GY. Translocation time values indicate that rare base-pairs can be successfully distinguished as the difference in their translocation times is very large for pure and B/N-doped γ-GY nanosheets. Meanwhile, sensing response values illustrated that pure and B-doped γ-GY are the best for G-5-hmCyt adsorption, while the N-doped γ-GY is the best for G-Cyt adsorption. The findings indicate that translocation times and sensing response can be used as detection indexes for pure and B/N doped γ-GY, which will provide a new way for experimental scientists to develop the biosensor components.

Aptamer-Based Switching System for Communication of Non-Interacting Proteins

Biological macromolecules, such as DNA, RNA, and proteins in living organisms, form an intricate network that plays a key role in many biological processes. Many attempts have been made to build new networks by connecting non-communicable proteins with network mediators, especially using antibodies. In this study, we devised an aptamer-based switching system that enables communication between non-interacting proteins. As a proof of concept, two proteins, Cas13a and T7 RNA polymerase (T7 RNAP), were rationally connected using an aptamer that specifically binds to T7 RNAP. The proposed switching system can be modulated in both signal-on and signal-off manners and its responsiveness to the target activator can be controlled by adjusting the reaction time. This study paves the way for the expansion of biological networks by mediating interactions between proteins using aptamers.

Redox Buffering Effects in Potentiometric Detection of DNA Using Thiol-Modified Gold Electrodes

Label-free potentiometric detection of DNA molecules using a field-effect transistor (FET) with a gold gate offers an electrical sensing platform for rapid, straightforward, and inexpensive analyses of nucleic acid samples. To induce DNA hybridization on the FET sensor surface to enable potentiometric detection, probe DNA that is complementary to the target DNA has to be immobilized on the FET gate surface. A common method for probe DNA functionalization is based on thiol–gold chemistry, immobilizing thiol-modified probe DNA on a gold gate with thiol–gold bonds. A self-assembled monolayer (SAM), based on the same thiol–gold chemistry, is also needed to passivate the rest of the gold gate surface to prevent non-specific adsorption and to enable favorable steric configuration of the probe DNA. Herein, the applicability of such FET-based potentiometric DNA sensing was carefully investigated, using a silicon nanoribbon FET with a gold-sensing gate modified with thiol–gold chemistry. We discover that the potential of the gold-sensing electrode is determined by the mixed potential of the gold–thiol and gold–oxygen redox interactions. This mixed potential gives rise to a redox buffer effect which buffers the change in the surface charge induced by the DNA hybridization, thus suppressing the potentiometric signal. Analogous redox buffer effects may also be present for other types of potentiometric detections of biomarkers based on thiol–gold chemistry.

Recent Advances in Electric-Double-Layer Transistors for Bio-Chemical Sensing Applications

As promising biochemical sensors, ion-sensitive field-effect transistors (ISFETs) are used widely in the growing field of biochemical sensing applications. Recently, a new type of field-effect transistor gated by ionic electrolytes has attracted intense attention due to the extremely strong electric-double-layer (EDL) gating effect. In such devices, the carrier density of the semiconductor channel can be effectively modulated by an ion-induced EDL capacitance at the semiconductor/electrolyte interface. With advantages of large specific capacitance, low operating voltage and sensitive interfacial properties, various EDL-based transistor (EDLT) devices have been developed for ultrasensitive portable sensing applications. In this article, we will review the recent progress of EDLT-based biochemical sensors. Starting with a brief introduction of the concepts of EDL capacitance and EDLT, we describe the material compositions and the working principle of EDLT devices. Moreover, the biochemical sensing performances of several important EDLTs are discussed in detail, including organic-based EDLTs, oxide-based EDLTs, nanomaterial-based EDLTs and neuromorphic EDLTs. Finally, the main challenges and development prospects of EDLT-based biochemical sensors are listed.

Top-Down Fabricated Silicon Nanowire Arrays for Field-Effect Detection of Prostate-Specific Antigen

Highly sensitive electrical detection of biomarkers for the early stage screening of cancer is desired for future, ultrafast diagnostic platforms. In the case of prostate cancer (PCa), the prostate-specific antigen (PSA) is of prime interest and its detection in combination with other PCa-relevant biomarkers in a multiplex approach is advised. Toward this goal, we demonstrate the label-free, potentiometric detection of PSA with silicon nanowire ion-sensitive field-effect transistor (Si NW-ISFET) arrays. To realize the field-effect detection, we utilized the DNA aptamer-receptors specific for PSA, which were covalently and site-specifically immobilized on Si NW-ISFETs. The platform was used for quantitative detection of PSA and the change in threshold voltage of the Si NW-ISEFTs was correlated with the concentration of PSA. Concentration-dependent measurements were done in a wide range of 1 pg/mL to 1 μg/mL, which covers the clinical range of interest. To confirm the PSA-DNA aptamer binding on the Si NW surfaces, a sandwich-immunoassay based on chemiluminescence was implemented. The electrical approach using the Si NW-ISFET platform shows a lower limit of detection and a wide dynamic range of the assay. In future, our platform should be utilized to detect multiple biomarkers in one assay to obtain more reliable information about cancer-related diseases.

Dynamic range extension of hybridization sensors

In hybridization based nucleic acid sensors the stringency of hybridization poses a challenge to design and experiment. For a given set of experimental parameters the affinity window of probe-target interaction is always limited and vice versa for a given probe set design, changes in experimental conditions can easily bring some measurements out of detection range. In this paper we introduce and apply a strategy to extend this dynamic range for affinity sensors, sensors which measure the amount of hybridized molecules after equilibrium is reached. The method relies on concepts of additivity of nucleic acids hybridization free energies and on equilibrium isotherms. It consists in combining the measurements from probes with different lengths, by appropriately rescaling the measured signals. We test the validity of the approach on experiments and show that by combining probes with hybridizing regions of length 21, 23 and 25 nucleotides we manage to extend the dynamic range of the intensity signals by a factor of 25. The presented concept is easy to extend, platform free and applies to any hybridization based affinity sensor.

Trapping of a single DNA molecule using nanoplasmonic structures for biosensor applications

Conventional optical trapping using a tightly focused beam is not suitable for trapping particles that are smaller than the diffraction limit because of the increasing need of the incident laser power that could produce permanent thermal damages. One of the current solutions to this problem is to intensify the local field enhancement by using nanoplasmonic structures without increasing the laser power. Nanoplasmonic tweezers have been used for various small molecules but there is no known report of trapping a single DNA molecule. In this paper, we present the trapping of a single DNA molecule using a nanohole created on a gold substrate. Furthermore, we show that the DNA of different lengths can be differentiated through the measurement of scattering signals leading to possible new DNA sensor applications.

Programmable ion-sensitive transistor interfaces. III. Design considerations, signal generation, and sensitivity enhancement

We report on factors that affect DNA hybridization detection using ion-sensitive field-effect transistors (ISFETs). Signal generation at the interface between the transistor and immobilized biomolecules is widely ascribed to unscreened molecular charges causing a shift in surface potential and hence the transistor output current. Traditionally, the interaction between DNA and the dielectric or metal sensing interface is modeled by treating the molecular layer as a sheet charge and the ionic profile with a Poisson-Boltzmann distribution. The surface potential under this scenario is described by the Graham equation. This approximation, however, often fails to explain large hybridization signals on the order of tens of mV. More realistic descriptions of the DNA-transistor interface which include factors such as ion permeation, exclusion, and packing constraints have been proposed with little or no corroboration against experimental findings. In this study, we examine such physical models by their assumptions, range of validity, and limitations. We compare simulations against experiments performed on electrolyte-oxide-semiconductor capacitors and foundry-ready floating-gate ISFETs. We find that with weakly charged interfaces (i.e., low intrinsic interface charge), pertinent to the surfaces used in this study, the best agreement between theory and experiment exists when ions are completely excluded from the DNA layer. The influence of various factors such as bulk pH, background salinity, chemical reactivity of surface groups, target molecule concentration, and surface coatings on signal generation is studied. Furthermore, in order to overcome Debye screening limited detection, we suggest two signal enhancement strategies. We first describe frequency domain biosensing, highlighting the ability to sort short DNA strands based on molecular length, and then describe DNA biosensing in multielectrolytes comprising trace amounts of higher-valency salt in a background of monovalent saline. Our study provides guidelines for optimized interface design, signal enhancement, and the interpretation of FET-based biosensor signals.

Photocontrolled adsorption of polyelectrolyte molecules on a silicon substrate

We report on a change in the properties of monomolecular films of polyelectrolyte molecules, induced by illuminating the silicon substrate on which they adsorb. It was found that under illumination the thickness of the adsorbed layer decreases by at least 27% and at the same time the roughness is significantly reduced in comparison to a layer adsorbed without irradiation. Furthermore, the homogeneity of the film topography and the surface potential is shown to be improved by illumination. The effect is explained by a change in surface charge density under irradiation of n- and p-type silicon wafers. The altered charge density in turn induces conformational changes of the adsorbing polyelectrolyte molecules. Their photocontrolled adsorption opens new possibilities for selective manipulation of adsorbed films. This possibility is of potential importance for many applications such as the production of well-defined coatings in biosensors or microelectronics.